Modeling energy transport in nanoscale materials is a challenging problem and an active research area. One of the main limitations in the current modeling techniques for energy transport at the nanoscale is that the time and size of systems that can be simulated is so small that the simulation of experimental setups cannot be achieved. The limitation in modeling techniques comes from exceedingly large time and length scales involved in materials, that are needed in order to properly predict diffusive events, such as heat and mass transport. In this work, we use a mixed atomic-kinematic thermo-chemo-mechanical formulation to describe non-equilibrium system to simulate energy transport at the nanoscale. Traditional force field methods are employed in order to compute equilibrium configurations in addition to phenomenological kinematic laws for heat and mass transport. We describe the methodology and show different test cases and transport simulations of nanoscale materials using the proposed methodology.